Re: [ccp4bb]: list of residues buried in an interface

["P.J.Briggs" <P.J.Briggs@dl.ac.uk>]

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Fred

I think AREAIMOL in CCP4 could also be used in DIFFMODE COMPARE to do
this, although it is very crude - you supply two PDB files for each
run of the program, one is the whole complex and the second contains
just one subunit. Then use a script like:

areaimol XYZIN complex.pdb XYZIN2 subunit.pdb XYZOUT diff.pdb <<eof
diffmode compare
output
end
eof

You can look at the output file ("diff.pdb") which should only list the
atoms which a) were common to the two files and b) have non-zero area
differences (i.e. those which are buried in the complex but exposed in
the subunit).

You can then see which residues were involved in the interaction.
Unfortunately these aren't tabulated or anything - I guess I should
write something into the next version which makes a nice table for you
automatically... ;)

Peter.

On Thu, 9 Aug 2001, Fred. Vellieux wrote:

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> 
> Dear CCP4BB subscribers,
> 
> Maybe this is just a wish that I have which is not yet fulfilled...
> 
> Is there some program around that takes a number of coordinate files
> (understand: PDB files) corresponding to an "aggregate" (e.g. a dimer)
> and to the separate subunits, and provides a table of the residues
> buried in the subunit-subunit interface(s)?
> 
> I know this can be done visually on the graphics station, using
> very high-tech supplementary equipment (paper + pencil). But having
> it done "automagically" sounds nice to me... laziness being a quality,
> of course.
> 
> Fred.
> 
> -- 
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> MP/H/0?*ZM_GS&C'30I,>S1G3UI>T-H;`!!>N'*JT1?[?;#OW[]UR'@YY2X`Z
> MN)5"J6`$X-<O3Q/),4@]C=2$")KC"37!"Z1L]XW(-8E&KIE9/0[=K]@C3[-#
> ?79H.\3W6F8,D<4WH4D.]E.>U+FCGZ3L6+P0_(.@T$```
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> 
> 

--
_____________________________________________________
Peter J Briggs, pjx@ccp4.ac.uk   Tel: +44 1925 603826
CCP4,           ccp4@ccp4.ac.uk  Fax: +44 1925 603825
                http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington   WA4 4AD